#!/bin/bash -e

function info() {
echo Usage: `basename $0` 'in.vcf' express
exit 1
}

while getopts  ":p:f:" opt; do
	case  $opt  in
		p) out_prefix=$OPTARG;;
		f) suffix=$OPTARG;;
		*) info;;
	esac
done
shift $(($OPTIND - 1))


if [ $# -lt 1 ]; then info; fi

. $var

tt="GEN[0].FREQ"

echo extractFields
$java_run/snpsift extractFields "$@" > $out_prefix.extract.txt

sed -i '1s/^#//;1s/dbNSFP_//g;1s/ANN\[0\]\./F_/g' $out_prefix.extract.txt

. $cmd_done
